Bioinformatics enables biotechnology and cancer research

Genomics and molecular biology has been a source of inspiration for biology and biotechnology research worldwide. Scientists and the researchers are unable to analyze this huge data manually so that innovative theraputical solutions have emerged for the data analysis. Bioinformatics come to the rescue of the scientists and researchers in digging the information efficiently. Bioinformatics is particularly capable of developing the next generation cancer research from the data and can come with innovative solutions to cure cancer.

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Human-Organoid Models: Accomplishments to Salvage Test-Animals

Late stage attritions in drug discovery are costly and consuming. Improbable response of test molecules acquired in non-human systems is attributed to be the major cause of clinical failures. While conventional in vitro methods of drug discovery do not truly represent the human system, the animal models used for in vivo validation are also genetically and phenotypically distant from humans. However, recent developments in organoid culture are motivating and elevate hopes for replacing test animals with artificial human tissue models. 

Possibility of creating functional tissue ex vivo has a potential to revolutionize the way human therapeutics is perceived. Not only will it bridge the gap between drug development and its clinical efficacy but also help strategizing regenerative medicine. Successful human-tissue surrogates would liberate test animals or at least minimize their use for research purposes. 

Evaluating the Impact of Different Factors on Voxel-Based Classification Methods of ADNI Structural MRI Brain Images

In this work we introduce the use of penalized logistic regression (PLR) to the problem of classification of MRI images and automatic detection of Alzheimer’s disease. Classification of sMRI is approached as a large scale regularization problem which uses voxels as input features. We evaluate how differences in sMRI pre-processing steps such as smoothing, normalization, and template selection affect the performance of high dimensional classification methods. 

In addition, we compared the relative performance of PLR to a different approach based on support vector machines. To study these questions we used data from the Alzheimer Disease Neuro imaging Initiative (ADNI). The ADNI project follows a protocol consisting of acquisition of two images in each session, image correction steps and further evaluation by experts to obtain the optimized images. We evaluated here the impact of this optimization process on the performance of high-dimensional machine learning techniques.

Likelihood Ratio Test of Hardy-Weinberg Equilibrium Using Uncertain Genotypes for Sibship Data

Testing for Hardy-Weinberg equilibrium of genotype frequencies is a crucial first step in the study of population genetics. In this paper, we develop an Expectation-Maximization algorithm to estimate the genotype frequencies for sibship data with genotype uncertainty. 

We also develop a likelihood ratio test of Hardy-Weinberg equilibrium for sibships with no parental genotypes available and with possible genotyping errors. Simulations show that our likelihood ratio test maintains valid control of the type I error rate and good statistical power. Finally, the likelihood ratio test is extended across strata when a sample is stratified by multiple ethnic populations with different genotype frequencies.

DNA/RNA Fragmentation and Cytolysis in Human Cancer Cells Treated with Diphthamide Nano Particles Derivatives

Molecular structure activity studies for some Diphthamide Nano particles derivatives indicate that the conformational characteristics along with the nature and position of the substituents on the Diphthamide Nano particles derivatives ring play an important role in their biological and biochemical activities. Therefore, we have calculated the optimized molecular geometries of some Diphthamide Nano particles derivatives. 

Calculations are carried out on the structures of these medical, medicinal and pharmaceutical Nano drugs using Hartree–Fock calculations and also Density Functional Theory (DFT) by performing HF, PM3, MM2, MM3, AM1, MP2, MP3, MP4, CCSD, CCSD(T), LDA, BVWN, BLYP and B3LYP levels of theory using the standard 31G, 6–31G*, 6–31+G*, 6–31G(3df, 3pd), 6–311G, 6–311G* and 6–311+G* basis sets of the Gaussian 09. The comparative heats of formation and Natural Bond Orbital (NBO) charges are calculated for these Diphthamide Nano particles derivatives. We have finally obtained some conformational rules in terms of the natures and positions of the substituents on the Diphthamide Nano particles derivatives ring.

Data Inventory for Cancer Patients Receiving Radiotherapy for Outcome Analysis and Modeling

Data collection for cancer patients is recognized as an important task in the USA, where the National Program of Cancer Registries (NPCR) administered by the Centers for Disease Control and Prevention collects data on the occurrence, type, extent, and location of the cancer, and the type of initial treatment. The International Consortium for Health Outcomes Measurements (ICHOM) aims at providing a global resource of in-use outcome measures and risk adjustment factors by medical condition and creating a global standard for measuring results. 

These initiatives will enable public health professionals to understand and address the cancer burden more effectively. We have recently proposed to use the pre-treatment, planning, and treatment outcomes data for cancer patients undergoing radiation therapy to provide guidelines for optimal choice of both radiation modality and planning for new patients. It is important to determine the most influential patient features (or their combinations) that has the strongest correlation with the outcomes. We propose an Overlap Volume Histogram as a valuable representation of size and shape for tumor and organs at risk important for planning.

A new sensitive and rapid assaying technique

Inspite of their low sensitivity compared to chemiluminescenceand fluorescence methods, Immunochromato graphic(IC) and Lateral flow (LF) test strips are widely used for the rapid detection of drugs, clinical factors, food safety etc. Recently American scientists developed adaptable rapid quantitation and multiplex detection sensitive assay for assaying clinical drugs,biomarkers, etc.

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A Similarity Retrieval Tool for Functional Magnetic Resonance Imaging Statistical Maps

We propose a method for retrieving similar functional magnetic resonance imaging (fMRI) statistical images given a query fMRI statistical image. Our method thresholds the voxels within those images and extracts spatially distinct regions from the voxels that remain. Each region is defined by a feature vector that contains the region centroid, the region area, the average activation value for all the voxels within that region, the variance of those activation values, the average distance of each voxel within that region to the region’s centroid, and the variance of the voxel’s distance to the region’s centroid. 

The similarity between two images is obtained by the summed minimum distance (SMD) of their constituent feature vectors. Results and conclusion. Our method is sensitive to similarities in brain activation patterns from members of the same data set. Using a subset of the features such as the centroid location and the average activation value (individually or in combination), maximized the sensitivity of our method. We also identified the similarity structure of the entire data set using those two features and the SMD.